Modeling residue usage in aligned protein sequences via maximum likelihood

Molecular Biology and Evolution
W J Bruno

Abstract

A computational method is presented for characterizing residue usage, i.e., site-specific residue frequencies, in aligned protein sequences. The method obtains frequency estimates that maximize the likelihood of the sequences in a simple model for sequence evolution, given a tree or a set of candidate trees computed by other methods. These maximum-likelihood frequencies constitute a profile of the sequences, and thus the method offers a rigorous alternative to sequence weighting for constructing such a profile. The ability of this method to discard misleading phylogenetic effects allows the biochemical propensities of different positions in a sequence to be more clearly observed and interpreted.

Citations

Nov 23, 2000·Current Opinion in Genetics & Development·J L Thorne
Sep 13, 2007·Heredity·M Anisimova, D A Liberles
Nov 9, 2004·Bioinformatics·Gavin E Crooks, Steven E Brenner
Dec 8, 2005·Bioinformatics·Tanja Gesell, Arndt von Haeseler
Aug 23, 2008·Bioinformatics·Le Si QuangNicolas Lartillot
May 16, 2006·Molecular Biology and Evolution·Richard A Goldstein, David D Pollock
Mar 6, 2008·Molecular Biology and Evolution·Bryan Kolaczkowski, Joseph W Thornton
Dec 13, 2012·Molecular Biology and Evolution·Chieh-Hsi WuAlexei J Drummond
Oct 15, 2008·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Si Quang LeOlivier Gascuel
Oct 5, 2006·BMC Bioinformatics·Peter S KlostermanIan Holmes
Jun 28, 2007·BMC Bioinformatics·Eric A Stone, Arend Sidow
Jan 18, 2011·BMC Evolutionary Biology·Béatrice Roure, Hervé Philippe
Feb 10, 2007·BMC Evolutionary Biology·Nicolas LartillotHervé Philippe
Nov 17, 2009·PLoS Computational Biology·Asif U TamuriRichard A Goldstein
Dec 2, 2011·PLoS Computational Biology·Michael E WallJohn Dunbar
Jul 6, 2007·PloS One·Jonathan CarlsonDavid Heckerman
Aug 12, 2009·PloS One·Robert K BradleyIan Holmes
Feb 8, 2005·Applied Bioinformatics·Rose HobermanRoni Rosenfeld
Feb 6, 2014·Journal of Structural and Functional Genomics·Bo Wang, Michael A Kennedy
Jul 17, 2003·Proteins·Bin Qian, Richard A Goldstein
Apr 9, 2016·Biology Direct·Leonardo de Oliveira Martins, David Posada
Feb 10, 2000·Molecular Biology and Evolution·W R AtchleyA W Dress
Dec 9, 2000·Molecular Biology and Evolution·D D PollockM P Cummings
Apr 17, 2002·Journal of Molecular Biology·I Holmes, G M Rubin
Dec 14, 2004·Molecular Biology and Evolution·C BlouinA J Roger
Mar 12, 2004·Molecular Biology and Evolution·Nicolas Lartillot, Hervé Philippe
Oct 21, 2005·Molecular Biology and Evolution·Vivek Gowri-Shankar, Magnus Rattray
Feb 28, 2019·BMC Evolutionary Biology·S Omar Kazmi, Nicolas Rodrigue
Feb 1, 2008·Molecular Biology and Evolution·Samuel Blanquart, Nicolas Lartillot
Nov 25, 2020·Journal of Molecular Evolution·Mackenzie M Johnson, Claus O Wilke
Dec 22, 2020·Virus Evolution·Vadim PullerRichard A Neher
May 30, 2021·BMC Bioinformatics·Nicola De MaioNick Goldman

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